Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2od6-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od6-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od6-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-3.6-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-3.6-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Tue 25 Dec 19:28:07 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od6-3.6-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 314 and 0 Target number of residues in the AU: 314 Target solvent content: 0.6528 Checking the provided sequence file Detected sequence length: 110 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 440 Adjusted target solvent content: 0.51 Input MTZ file: 2od6-3.6-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 19 Cell parameters: 36.403 92.834 144.837 90.000 90.000 90.000 Input sequence file: 2od6-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3520 target number of atoms Had to go as low as 0.75 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 29.066 3.600 Wilson plot Bfac: 79.53 6060 reflections ( 98.76 % complete ) and 0 restraints for refining 3886 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3392 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3384 (Rfree = 0.000) for 3886 atoms. Found 24 (24 requested) and removed 18 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.61 3.56 Search for helices and strands: 0 residues in 0 chains, 3993 seeds are put forward NCS extension: 0 residues added, 3993 seeds are put forward Round 1: 188 peptides, 36 chains. Longest chain 16 peptides. Score 0.333 Round 2: 255 peptides, 38 chains. Longest chain 19 peptides. Score 0.517 Round 3: 262 peptides, 35 chains. Longest chain 16 peptides. Score 0.571 Round 4: 272 peptides, 28 chains. Longest chain 23 peptides. Score 0.669 Round 5: 298 peptides, 32 chains. Longest chain 23 peptides. Score 0.684 Taking the results from Round 5 Chains 32, Residues 266, Estimated correctness of the model 44.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6933 restraints for refining 3188 atoms. 5901 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3047 (Rfree = 0.000) for 3188 atoms. Found 12 (20 requested) and removed 25 (10 requested) atoms. Cycle 2: After refmac, R = 0.3011 (Rfree = 0.000) for 3119 atoms. Found 14 (20 requested) and removed 20 (10 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.2556 (Rfree = 0.000) for 3066 atoms. Found 3 (19 requested) and removed 16 (9 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.2763 (Rfree = 0.000) for 3029 atoms. Found 5 (19 requested) and removed 18 (9 requested) atoms. Cycle 5: After refmac, R = 0.2803 (Rfree = 0.000) for 3002 atoms. Found 5 (19 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.55 3.50 Search for helices and strands: 0 residues in 0 chains, 3127 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 3150 seeds are put forward Round 1: 245 peptides, 42 chains. Longest chain 20 peptides. Score 0.436 Round 2: 265 peptides, 36 chains. Longest chain 26 peptides. Score 0.567 Round 3: 244 peptides, 34 chains. Longest chain 25 peptides. Score 0.535 Round 4: 238 peptides, 32 chains. Longest chain 15 peptides. Score 0.543 Round 5: 238 peptides, 30 chains. Longest chain 25 peptides. Score 0.567 Taking the results from Round 5 Chains 30, Residues 208, Estimated correctness of the model 1.3 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 7273 restraints for refining 3191 atoms. 6471 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3135 (Rfree = 0.000) for 3191 atoms. Found 20 (20 requested) and removed 29 (10 requested) atoms. Cycle 7: After refmac, R = 0.2975 (Rfree = 0.000) for 3152 atoms. Found 12 (20 requested) and removed 26 (10 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.3067 (Rfree = 0.000) for 3111 atoms. Found 20 (20 requested) and removed 22 (10 requested) atoms. Cycle 9: After refmac, R = 0.2974 (Rfree = 0.000) for 3087 atoms. Found 19 (19 requested) and removed 21 (9 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.2796 (Rfree = 0.000) for 3067 atoms. Found 10 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.59 3.54 Search for helices and strands: 0 residues in 0 chains, 3202 seeds are put forward NCS extension: 17 residues added (1 deleted due to clashes), 3219 seeds are put forward Round 1: 219 peptides, 42 chains. Longest chain 9 peptides. Score 0.352 Round 2: 237 peptides, 37 chains. Longest chain 14 peptides. Score 0.478 Round 3: 252 peptides, 35 chains. Longest chain 16 peptides. Score 0.545 Round 4: 236 peptides, 35 chains. Longest chain 17 peptides. Score 0.500 Round 5: 236 peptides, 31 chains. Longest chain 26 peptides. Score 0.550 Taking the results from Round 5 Chains 31, Residues 205, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 7319 restraints for refining 3189 atoms. 6530 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2986 (Rfree = 0.000) for 3189 atoms. Found 17 (20 requested) and removed 32 (10 requested) atoms. Failed to save intermediate PDB Cycle 12: After refmac, R = 0.3191 (Rfree = 0.000) for 3153 atoms. Found 20 (20 requested) and removed 21 (10 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2851 (Rfree = 0.000) for 3122 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2867 (Rfree = 0.000) for 3104 atoms. Found 20 (20 requested) and removed 17 (10 requested) atoms. Cycle 15: After refmac, R = 0.2775 (Rfree = 0.000) for 3095 atoms. Found 14 (19 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.57 3.52 Search for helices and strands: 0 residues in 0 chains, 3202 seeds are put forward NCS extension: 36 residues added (2 deleted due to clashes), 3238 seeds are put forward Round 1: 192 peptides, 39 chains. Longest chain 11 peptides. Score 0.303 Round 2: 212 peptides, 35 chains. Longest chain 13 peptides. Score 0.427 Round 3: 222 peptides, 36 chains. Longest chain 15 peptides. Score 0.445 Round 4: 229 peptides, 31 chains. Longest chain 20 peptides. Score 0.531 Round 5: 233 peptides, 35 chains. Longest chain 20 peptides. Score 0.491 Taking the results from Round 4 Chains 31, Residues 198, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6060 reflections ( 98.76 % complete ) and 7057 restraints for refining 3187 atoms. 6296 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2962 (Rfree = 0.000) for 3187 atoms. Found 20 (20 requested) and removed 32 (10 requested) atoms. Cycle 17: After refmac, R = 0.2864 (Rfree = 0.000) for 3146 atoms. Found 19 (20 requested) and removed 20 (10 requested) atoms. Cycle 18: After refmac, R = 0.2846 (Rfree = 0.000) for 3133 atoms. Found 20 (20 requested) and removed 23 (10 requested) atoms. Cycle 19: After refmac, R = 0.2969 (Rfree = 0.000) for 3116 atoms. Found 20 (20 requested) and removed 29 (10 requested) atoms. Cycle 20: After refmac, R = 0.2862 (Rfree = 0.000) for 3084 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 3212 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 3238 seeds are put forward Round 1: 155 peptides, 33 chains. Longest chain 10 peptides. Score 0.259 Round 2: 175 peptides, 34 chains. Longest chain 11 peptides. Score 0.317 Round 3: 185 peptides, 32 chains. Longest chain 16 peptides. Score 0.382 Round 4: 178 peptides, 28 chains. Longest chain 19 peptides. Score 0.417 Round 5: 198 peptides, 32 chains. Longest chain 18 peptides. Score 0.424 Taking the results from Round 5 Chains 32, Residues 166, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6060 reflections ( 98.76 % complete ) and 7271 restraints for refining 3191 atoms. 6639 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3074 (Rfree = 0.000) for 3191 atoms. Found 20 (20 requested) and removed 31 (10 requested) atoms. Cycle 22: After refmac, R = 0.2991 (Rfree = 0.000) for 3154 atoms. Found 20 (20 requested) and removed 25 (10 requested) atoms. Cycle 23: After refmac, R = 0.2612 (Rfree = 0.000) for 3139 atoms. Found 11 (20 requested) and removed 17 (10 requested) atoms. Cycle 24: After refmac, R = 0.2603 (Rfree = 0.000) for 3121 atoms. Found 10 (20 requested) and removed 15 (10 requested) atoms. Cycle 25: After refmac, R = 0.3093 (Rfree = 0.000) for 3107 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.58 3.53 Search for helices and strands: 0 residues in 0 chains, 3200 seeds are put forward NCS extension: 26 residues added (1 deleted due to clashes), 3226 seeds are put forward Round 1: 160 peptides, 32 chains. Longest chain 8 peptides. Score 0.293 Round 2: 188 peptides, 33 chains. Longest chain 14 peptides. Score 0.377 Round 3: 205 peptides, 34 chains. Longest chain 16 peptides. Score 0.419 Round 4: 193 peptides, 29 chains. Longest chain 15 peptides. Score 0.451 Round 5: 192 peptides, 33 chains. Longest chain 13 peptides. Score 0.391 Taking the results from Round 4 Chains 29, Residues 164, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 7329 restraints for refining 3191 atoms. 6702 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3318 (Rfree = 0.000) for 3191 atoms. Found 20 (20 requested) and removed 34 (10 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.3164 (Rfree = 0.000) for 3158 atoms. Found 20 (20 requested) and removed 24 (10 requested) atoms. Cycle 28: After refmac, R = 0.2945 (Rfree = 0.000) for 3137 atoms. Found 20 (20 requested) and removed 18 (10 requested) atoms. Cycle 29: After refmac, R = 0.2617 (Rfree = 0.000) for 3129 atoms. Found 10 (20 requested) and removed 14 (10 requested) atoms. Cycle 30: After refmac, R = 0.2812 (Rfree = 0.000) for 3114 atoms. Found 19 (20 requested) and removed 21 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.78 3.73 Search for helices and strands: 0 residues in 0 chains, 3203 seeds are put forward NCS extension: 19 residues added (0 deleted due to clashes), 3222 seeds are put forward Round 1: 138 peptides, 31 chains. Longest chain 6 peptides. Score 0.225 Round 2: 159 peptides, 32 chains. Longest chain 7 peptides. Score 0.289 Round 3: 156 peptides, 31 chains. Longest chain 8 peptides. Score 0.294 Round 4: 162 peptides, 30 chains. Longest chain 13 peptides. Score 0.332 Round 5: 169 peptides, 31 chains. Longest chain 12 peptides. Score 0.341 Taking the results from Round 5 Chains 31, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 7334 restraints for refining 3129 atoms. 6813 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3444 (Rfree = 0.000) for 3129 atoms. Found 20 (20 requested) and removed 38 (10 requested) atoms. Cycle 32: After refmac, R = 0.2989 (Rfree = 0.000) for 3088 atoms. Found 19 (19 requested) and removed 19 (9 requested) atoms. Cycle 33: After refmac, R = 0.2882 (Rfree = 0.000) for 3075 atoms. Found 19 (19 requested) and removed 20 (9 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2751 (Rfree = 0.000) for 3066 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 35: After refmac, R = 0.2793 (Rfree = 0.000) for 3065 atoms. Found 19 (19 requested) and removed 17 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.55 Search for helices and strands: 0 residues in 0 chains, 3151 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 3154 seeds are put forward Round 1: 136 peptides, 30 chains. Longest chain 7 peptides. Score 0.233 Round 2: 158 peptides, 32 chains. Longest chain 8 peptides. Score 0.286 Round 3: 157 peptides, 30 chains. Longest chain 10 peptides. Score 0.313 Round 4: 164 peptides, 31 chains. Longest chain 11 peptides. Score 0.323 Round 5: 150 peptides, 29 chains. Longest chain 9 peptides. Score 0.303 Taking the results from Round 4 Chains 31, Residues 133, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6956 restraints for refining 3043 atoms. 6455 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2907 (Rfree = 0.000) for 3043 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 37: After refmac, R = 0.3074 (Rfree = 0.000) for 3022 atoms. Found 19 (19 requested) and removed 27 (9 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.2863 (Rfree = 0.000) for 3007 atoms. Found 19 (19 requested) and removed 13 (9 requested) atoms. Cycle 39: After refmac, R = 0.2857 (Rfree = 0.000) for 3002 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. Cycle 40: After refmac, R = 0.2850 (Rfree = 0.000) for 3003 atoms. Found 19 (19 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 3088 seeds are put forward NCS extension: 6 residues added (1 deleted due to clashes), 3094 seeds are put forward Round 1: 148 peptides, 34 chains. Longest chain 8 peptides. Score 0.215 Round 2: 169 peptides, 35 chains. Longest chain 10 peptides. Score 0.280 Round 3: 170 peptides, 34 chains. Longest chain 14 peptides. Score 0.299 Round 4: 181 peptides, 35 chains. Longest chain 12 peptides. Score 0.323 Round 5: 180 peptides, 34 chains. Longest chain 12 peptides. Score 0.335 Taking the results from Round 5 Chains 34, Residues 146, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6060 reflections ( 98.76 % complete ) and 6950 restraints for refining 3080 atoms. 6400 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2908 (Rfree = 0.000) for 3080 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.3122 (Rfree = 0.000) for 3052 atoms. Found 19 (19 requested) and removed 32 (9 requested) atoms. Cycle 43: After refmac, R = 0.2907 (Rfree = 0.000) for 3008 atoms. Found 19 (19 requested) and removed 22 (9 requested) atoms. Cycle 44: After refmac, R = 0.2901 (Rfree = 0.000) for 2986 atoms. Found 19 (19 requested) and removed 15 (9 requested) atoms. Cycle 45: After refmac, R = 0.2758 (Rfree = 0.000) for 2980 atoms. Found 19 (19 requested) and removed 12 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.57 3.52 Search for helices and strands: 0 residues in 0 chains, 3072 seeds are put forward NCS extension: 11 residues added (0 deleted due to clashes), 3083 seeds are put forward Round 1: 106 peptides, 22 chains. Longest chain 7 peptides. Score 0.248 Round 2: 128 peptides, 26 chains. Longest chain 9 peptides. Score 0.268 Round 3: 139 peptides, 28 chains. Longest chain 8 peptides. Score 0.278 Round 4: 144 peptides, 27 chains. Longest chain 11 peptides. Score 0.313 Round 5: 135 peptides, 27 chains. Longest chain 9 peptides. Score 0.279 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2od6-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6060 reflections ( 98.76 % complete ) and 6468 restraints for refining 2911 atoms. 6027 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2910 (Rfree = 0.000) for 2911 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.2853 (Rfree = 0.000) for 2881 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.2775 (Rfree = 0.000) for 2863 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.2692 (Rfree = 0.000) for 2845 atoms. Found 0 (18 requested) and removed 9 (9 requested) atoms. Writing output files ... Failed to save intermediate PDB TimeTaking 56.65